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// Copyright 2013 Calvin Morrison
#include <errno.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "kmer_utils.h"
unsigned long position = 0;
int main(int argc, char **argv) {
char *line = NULL;
size_t len = 0;
ssize_t read;
if(argc != 3) {
printf("Please supply a filename and a kmer\n");
exit(EXIT_FAILURE);
}
FILE *fh = fopen(argv[1], "r" );
if(fh == NULL) {
fprintf(stderr, "Error opening %s - %s\n", argv[1], strerror(errno));
exit(EXIT_FAILURE);
}
unsigned long kmer = atoi(argv[2]);
if(kmer == 0) {
fprintf(stderr, "Error: invalid kmer.\n");
exit(EXIT_FAILURE);
}
const unsigned long width = (unsigned long)1 << (kmer * 2);
unsigned long long *counts = malloc((width+ 1) * sizeof(unsigned long long));
if(counts == NULL)
exit(EXIT_FAILURE);
while ((read = getline(&line, &len, fh)) != -1) {
if(line[0] != '>' && (read > kmer)) {
unsigned int i = 0;
unsigned long total = 0;
// reset our count matrix to zero
memset(counts, 0, width * sizeof(unsigned long long));
for(i = 0; i < read; i++) {
line[i] = alpha[(int)line[i]];
}
for(i = 0; i < read - kmer; i++) {
counts[num_to_index(&line[i],kmer, width)]++;
}
for(i = 0; i < width; i++)
total += counts[i];
for(i = 0; i < width - 1; i++)
printf("%llu\t", counts[i]);
printf("%llu\n", counts[width - 1]);
}
}
free(counts);
free(line);
return EXIT_SUCCESS;
}
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